Thank you Bill.
I guess I do not understand the problem of duplicates in leap. From your
email it seems that the residue number, res name and atom name (combination)
must be unique.
At the moment in my .pdb I have the atom numbers 1- 13440 (60x224), though
each dimer of 224 atoms is separated by TER, resname LIG (for all dimers)
and residue number 1 (again for all dimers). So for the combination of these
three fields there should be no duplicates.
I actually have never been able to load a .pdb file using loadpdb where the
format has been read without errors by leap. Is there an example .pdb file
anywhere that is definitely read in loadpdb without any error? (I try even
1FKO_trunc_sus.pdb from
http://ambermd.org/tutorials/basic/tutorial4b/ and
get errors also, using amber 10) And/or a code available to ensure .pdb
formatting is agreeable in leap?
With thanks,
Jenny
-----Original Message-----
From: Bill Ross [mailto:ross.cgl.ucsf.EDU]
Sent: Tuesday, November 08, 2011 11:42 AM
To: amber.ambermd.org
Subject: Re: [AMBER] addles "old coordinate file not specified"
> there appears to be trouble with duplicate atom names.
Since you simulated the dimer itself already, the dimer itself is presumably
not the problem, just the 'big' pdb file. To manually perform the same check
as leap, you could try something like this:
$ awk '{print $1,$2,$3}' big.pdb | sort | uniq -c | awk '$1 > 1'
where instead of the first $1,$2,$3 you use the actual field numbers for
residue number, res name, and atom name (counting from 1). This should just
confirm the duplicates that leap is seeing, pointing to what needs fixing.
Bill
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Received on Tue Nov 08 2011 - 10:30:03 PST
